-
1
-
-
0000025419
-
A method for testing the assumption of phylogenetic independence in comparative data
-
Abouheif, E. (1999) A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research, 1, 895-909.
-
(1999)
Evolutionary Ecology Research
, vol.1
, pp. 895-909
-
-
Abouheif, E.1
-
2
-
-
78149306494
-
Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load
-
Alizon, S., von Wyl, V., Stadler, T., Kouyos, R.D., Yerly, S., Hirschel, B. et al. (2010) Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLoS Pathogens, 6, e1001123.
-
(2010)
PLoS Pathogens
, vol.6
, pp. e1001123
-
-
Alizon, S.1
von Wyl, V.2
Stadler, T.3
Kouyos, R.D.4
Yerly, S.5
Hirschel, B.6
-
3
-
-
84865475040
-
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
-
Baele, G., Lemey, P., Bedford, T., Rambaut, A., Suchard, M.A. & Alekseyenko, A.V. (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Molecular Biology and Evolution, 29, 2157-2167.
-
(2012)
Molecular Biology and Evolution
, vol.29
, pp. 2157-2167
-
-
Baele, G.1
Lemey, P.2
Bedford, T.3
Rambaut, A.4
Suchard, M.A.5
Alekseyenko, A.V.6
-
4
-
-
33845898805
-
Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes
-
Barker, D., Meade, A. & Pagel, M. (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics, 23, 14-20.
-
(2007)
Bioinformatics
, vol.23
, pp. 14-20
-
-
Barker, D.1
Meade, A.2
Pagel, M.3
-
5
-
-
84898728051
-
Integrating influenza antigenic dynamics with molecular evolution
-
Bedford, T., Suchard, M.A., Lemey, P., Dudas, G., Gregory, V., Hay, A.J. et al. (2014) Integrating influenza antigenic dynamics with molecular evolution. Elife, 3, e01914.
-
(2014)
Elife
, vol.3
, pp. e01914
-
-
Bedford, T.1
Suchard, M.A.2
Lemey, P.3
Dudas, G.4
Gregory, V.5
Hay, A.J.6
-
6
-
-
0043092351
-
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
-
Beerenwinkel, N., Däumer, M., Oette, M., Korn, K., Hoffmann, D., Kaiser, R., Lengauer, T., Selbig, J. & Walter, H. (2003) Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Research, 31, 3850-3855.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3850-3855
-
-
Beerenwinkel, N.1
Däumer, M.2
Oette, M.3
Korn, K.4
Hoffmann, D.5
Kaiser, R.6
Lengauer, T.7
Selbig, J.8
Walter, H.9
-
7
-
-
84906783353
-
FNN: Fast Nearest Neighbor Search Algorithms and Applications
-
R package version 1.1
-
Beygelzimer, A., Kakadet, S., Langford, J., Arya, S., Mount, D. & Li, S. (2013) FNN: Fast Nearest Neighbor Search Algorithms and Applications. R package version 1.1. http://CRAN.R-project.org/package=FNN.
-
(2013)
-
-
Beygelzimer, A.1
Kakadet, S.2
Langford, J.3
Arya, S.4
Mount, D.5
Li, S.6
-
8
-
-
80053959139
-
Spread: spatial phylogenetic reconstruction of evolutionary dynamics
-
Bielejec, F., Rambaut, A., Suchard, M.A. & Lemey, P. (2011) Spread: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics, 27, 2910-2912.
-
(2011)
Bioinformatics
, vol.27
, pp. 2910-2912
-
-
Bielejec, F.1
Rambaut, A.2
Suchard, M.A.3
Lemey, P.4
-
9
-
-
0038325772
-
Testing for phylogenetic signal in comparative data: behavioral traits are more labile
-
Blomberg, S.P., Garland Jr, T. & Ives, A.R. (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution, 57, 717-745.
-
(2003)
Evolution
, vol.57
, pp. 717-745
-
-
Blomberg, S.P.1
Garland Jr, T.2
Ives, A.R.3
-
11
-
-
84883003232
-
Evidence for a continuous drift of the HIV-1 species towards higher resistance to neutralizing antibodies over the course of the epidemic
-
Bouvin-Pley, M., Morgand, M., Moreau, A., Jestin, P., Simonnet, C., Tran, L. et al. (2013) Evidence for a continuous drift of the HIV-1 species towards higher resistance to neutralizing antibodies over the course of the epidemic. PLoS Pathogens, 9, e1003477.
-
(2013)
PLoS Pathogens
, vol.9
, pp. e1003477
-
-
Bouvin-Pley, M.1
Morgand, M.2
Moreau, A.3
Jestin, P.4
Simonnet, C.5
Tran, L.6
-
12
-
-
77956425857
-
Adaptation of HIV-1 envelope gp120 to humoral immunity at a population level
-
Bunnik, E.M., Euler, Z., Welkers, M.R.A., Boeser-Nunnink, B.D.M., Grijsen, M.L., Prins, J.M. & Schuitemaker, H. (2010) Adaptation of HIV-1 envelope gp120 to humoral immunity at a population level. Nature Medicine, 16, 995-997.
-
(2010)
Nature Medicine
, vol.16
, pp. 995-997
-
-
Bunnik, E.M.1
Euler, Z.2
Welkers, M.R.A.3
Boeser-Nunnink, B.D.M.4
Grijsen, M.L.5
Prins, J.M.6
Schuitemaker, H.7
-
13
-
-
11944264347
-
Phylogenetic comparative analysis: a modeling approach for adaptive evolution
-
Butler, M. & King, A. (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist, 164, 683-695.
-
(2004)
American Naturalist
, vol.164
, pp. 683-695
-
-
Butler, M.1
King, A.2
-
14
-
-
0000043041
-
Some matrix-variate distribution theory: notational considerations and a bayesian application
-
Dawid, A.P. (1981) Some matrix-variate distribution theory: notational considerations and a bayesian application. Biometrika, 68, 265-274.
-
(1981)
Biometrika
, vol.68
, pp. 265-274
-
-
Dawid, A.P.1
-
15
-
-
84864530626
-
Bayesian phylogenetics with beauti and the beast 1.7
-
Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. (2012) Bayesian phylogenetics with beauti and the beast 1.7. Molecular Biology and Evolution, 29, 1969-1973.
-
(2012)
Molecular Biology and Evolution
, vol.29
, pp. 1969-1973
-
-
Drummond, A.J.1
Suchard, M.A.2
Xie, D.3
Rambaut, A.4
-
16
-
-
79960385535
-
Activity of broadly neutralizing antibodies, including PG9, PG16, and VRC01, against recently transmitted subtype B HIV-1 variants from early and late in the epidemic
-
Euler, Z., Bunnik, E.M., Burger, J.A., Boeser-Nunnink, B.D.M., Grijsen, M.L., Prins, J.M. & Schuitemaker, H. (2011) Activity of broadly neutralizing antibodies, including PG9, PG16, and VRC01, against recently transmitted subtype B HIV-1 variants from early and late in the epidemic. Journal of Virology, 85, 7236-7245.
-
(2011)
Journal of Virology
, vol.85
, pp. 7236-7245
-
-
Euler, Z.1
Bunnik, E.M.2
Burger, J.A.3
Boeser-Nunnink, B.D.M.4
Grijsen, M.L.5
Prins, J.M.6
Schuitemaker, H.7
-
17
-
-
0022203256
-
Phylogenies and the comparative method
-
Felsenstein, J. (1985) Phylogenies and the comparative method. American Naturalist, 125, 1-15.
-
(1985)
American Naturalist
, vol.125
, pp. 1-15
-
-
Felsenstein, J.1
-
18
-
-
84896918882
-
Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective
-
Fraser, C., Lythgoe, K., Leventhal, G.E., Shirreff, G., Hollingsworth, T.D., Alizon, S. & Bonhoeffer, S. (2014) Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science, 343, 1243727.
-
(2014)
Science
, vol.343
, pp. 1243727
-
-
Fraser, C.1
Lythgoe, K.2
Leventhal, G.E.3
Shirreff, G.4
Hollingsworth, T.D.5
Alizon, S.6
Bonhoeffer, S.7
-
19
-
-
0036920097
-
Phylogenetic analysis and comparative data: a test and review of evidence
-
Freckleton, R.P., Harvey, P.H. & Pagel, M. (2002) Phylogenetic analysis and comparative data: a test and review of evidence. American Naturalist, 160, 712-726.
-
(2002)
American Naturalist
, vol.160
, pp. 712-726
-
-
Freckleton, R.P.1
Harvey, P.H.2
Pagel, M.3
-
20
-
-
0346373759
-
Unifying the epidemiological and evolutionary dynamics of pathogens
-
Grenfell, B.T., Pybus, O.G., Gog, J.R., Wood, J.L.N., Daly, J.M., Mumford, J.A. & Holmes, E.C. (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science, 303, 327-332.
-
(2004)
Science
, vol.303
, pp. 327-332
-
-
Grenfell, B.T.1
Pybus, O.G.2
Gog, J.R.3
Wood, J.L.N.4
Daly, J.M.5
Mumford, J.A.6
Holmes, E.C.7
-
21
-
-
33846817277
-
Time squared: repeated measures on phylogenies
-
Guo, H., Weiss, R.E., Gu, X. & Suchard, M.A. (2007) Time squared: repeated measures on phylogenies. Molecular Biology and Evolution, 24, 352-362.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 352-362
-
-
Guo, H.1
Weiss, R.E.2
Gu, X.3
Suchard, M.A.4
-
22
-
-
0030772835
-
Stabilizing selection and the comparative analysis of adaptation
-
Hansen, T. (1997) Stabilizing selection and the comparative analysis of adaptation. Evolution, 52, 1341-1351.
-
(1997)
Evolution
, vol.52
, pp. 1341-1351
-
-
Hansen, T.1
-
23
-
-
37549027209
-
Geiger: investigating evolutionary radiations
-
Harmon, L.J., Weir, J.T., Brock, C.D., Glor, R.E. & Challenger, W. (2008) Geiger: investigating evolutionary radiations. Bioinformatics, 24, 129-131.
-
(2008)
Bioinformatics
, vol.24
, pp. 129-131
-
-
Harmon, L.J.1
Weir, J.T.2
Brock, C.D.3
Glor, R.E.4
Challenger, W.5
-
24
-
-
84903519837
-
Clinical applications of pathogen phylogenies
-
Hartfield, M., Murall, C.L. & Alizon, S. (2014) Clinical applications of pathogen phylogenies. Trends in Molecular Medicine, 20, 394-404.
-
(2014)
Trends in Molecular Medicine
, vol.20
, pp. 394-404
-
-
Hartfield, M.1
Murall, C.L.2
Alizon, S.3
-
25
-
-
0025924711
-
Comparative methods for explaining adaptations
-
Harvey, P.H. & Purvis, A. (1991) Comparative methods for explaining adaptations. Nature, 351, 619-624.
-
(1991)
Nature
, vol.351
, pp. 619-624
-
-
Harvey, P.H.1
Purvis, A.2
-
26
-
-
0030343462
-
Distinguishing "missing at random" and "missing completely at random"
-
Heitjan, D.F. & Basu, S. (1996) Distinguishing "missing at random" and "missing completely at random". American Statistician, 50, 207-213.
-
(1996)
American Statistician
, vol.50
, pp. 207-213
-
-
Heitjan, D.F.1
Basu, S.2
-
27
-
-
84901679825
-
The contribution of viral genotype to plasma viral set-point in HIV infection
-
Hodcroft, E., Hadfield, J.D., Fearnhill, E., Phillips, A., Dunn, D., O'Shea, S. et al. (2014) The contribution of viral genotype to plasma viral set-point in HIV infection. PLoS Pathogens, 10, e1004112.
-
(2014)
PLoS Pathogens
, vol.10
, pp. e1004112
-
-
Hodcroft, E.1
Hadfield, J.D.2
Fearnhill, E.3
Phillips, A.4
Dunn, D.5
O'Shea, S.6
-
28
-
-
77954059111
-
HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda
-
Hollingsworth, T.D., Laeyendecker, O., Shirreff, G., Donnelly, C.A., Serwadda, D., Wawer, M.J. et al. (2010) HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda. PLoS Pathogens, 6, e1000876.
-
(2010)
PLoS Pathogens
, vol.6
, pp. e1000876
-
-
Hollingsworth, T.D.1
Laeyendecker, O.2
Shirreff, G.3
Donnelly, C.A.4
Serwadda, D.5
Wawer, M.J.6
-
29
-
-
84885693840
-
Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution
-
Hool, A., Leventhal, G.E. & Bonhoeffer, S. (2013) Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution. Epidemics, 5, 174-180.
-
(2013)
Epidemics
, vol.5
, pp. 174-180
-
-
Hool, A.1
Leventhal, G.E.2
Bonhoeffer, S.3
-
30
-
-
1242276567
-
The phylogenetic mixed model
-
Housworth, E.A., Martins, E.P. & Lynch, M. (2004) The phylogenetic mixed model. American Naturalist, 163, 84-96.
-
(2004)
American Naturalist
, vol.163
, pp. 84-96
-
-
Housworth, E.A.1
Martins, E.P.2
Lynch, M.3
-
31
-
-
63949087100
-
Adaptation of HIV-1 to human leukocyte antigen class I
-
Kawashima, Y., Pfafferott, K., Frater, J., Matthews, P., Payne, R., Addo, M. et al. (2009) Adaptation of HIV-1 to human leukocyte antigen class I. Nature, 458, 641-645.
-
(2009)
Nature
, vol.458
, pp. 641-645
-
-
Kawashima, Y.1
Pfafferott, K.2
Frater, J.3
Matthews, P.4
Payne, R.5
Addo, M.6
-
32
-
-
84888024210
-
Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution
-
Koel, B.F., Burke, D.F., Bestebroer, T.M., van der Vliet, S., Zondag, G.C.M., Vervaet, G. et al. (2013) Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution. Science, 342, 976-979.
-
(2013)
Science
, vol.342
, pp. 976-979
-
-
Koel, B.F.1
Burke, D.F.2
Bestebroer, T.M.3
van der Vliet, S.4
Zondag, G.C.M.5
Vervaet, G.6
-
33
-
-
77951882045
-
Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland
-
Kouyos, R.D., von Wyl, V., Yerly, S., Böni, J., Taffè, P., Shah, C. et al. (2010) Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. Journal of Infectious Diseases, 201, 1488-1497.
-
(2010)
Journal of Infectious Diseases
, vol.201
, pp. 1488-1497
-
-
Kouyos, R.D.1
von Wyl, V.2
Yerly, S.3
Böni, J.4
Taffè, P.5
Shah, C.6
-
34
-
-
77953916828
-
HIV RNA levels in transmission sources only weakly predict plasma viral load in recipients
-
van der Kuyl, A.C., Jurriaans, S., Pollakis, G., Bakker, M. & Cornelissen, M. (2010) HIV RNA levels in transmission sources only weakly predict plasma viral load in recipients. AIDS, 24, 1607-1608.
-
(2010)
AIDS
, vol.24
, pp. 1607-1608
-
-
van der Kuyl, A.C.1
Jurriaans, S.2
Pollakis, G.3
Bakker, M.4
Cornelissen, M.5
-
35
-
-
34547403540
-
Predictors of disease progression in HIV infection: a review
-
Langford, S.E., Ananworanich, J. & Cooper, D.A. (2007) Predictors of disease progression in HIV infection: a review. AIDS Research and Therapy, 4, 11.
-
(2007)
AIDS Research and Therapy
, vol.4
, pp. 11
-
-
Langford, S.E.1
Ananworanich, J.2
Cooper, D.A.3
-
36
-
-
46149108174
-
Morphometrics of the avian small intestine compared with that of nonflying mammals: a phylogenetic approach
-
Lavin, S.R., Karasov, W.H., Ives, A.R., Middleton, K.M. & Garland Jr, T. (2008) Morphometrics of the avian small intestine compared with that of nonflying mammals: a phylogenetic approach. Physiological and Biochemical Zoology, 81, 526-550.
-
(2008)
Physiological and Biochemical Zoology
, vol.81
, pp. 526-550
-
-
Lavin, S.R.1
Karasov, W.H.2
Ives, A.R.3
Middleton, K.M.4
Garland Jr, T.5
-
37
-
-
33750297873
-
HIV evolutionary dynamics within and among hosts
-
Lemey, P., Rambaut, A. & Pybus, O.G. (2006) HIV evolutionary dynamics within and among hosts. AIDS Reviews, 8, 125-140.
-
(2006)
AIDS Reviews
, vol.8
, pp. 125-140
-
-
Lemey, P.1
Rambaut, A.2
Pybus, O.G.3
-
38
-
-
70349675664
-
Bayesian phylogeography finds its root
-
Lemey, P., Rambaut, A., Drummond, A. & Suchard, M. (2009) Bayesian phylogeography finds its root. PLoS Computational Biology, 5, e1000520.
-
(2009)
PLoS Computational Biology
, vol.5
, pp. e1000520
-
-
Lemey, P.1
Rambaut, A.2
Drummond, A.3
Suchard, M.4
-
39
-
-
77955011960
-
Phylogeography takes a relaxed random walk in continuous space and time
-
Lemey, P., Rambaut, A., Welch, J.J. & Suchard, M.A. (2010) Phylogeography takes a relaxed random walk in continuous space and time. Molecular Biology and Evolution, 27, 1877-1885.
-
(2010)
Molecular Biology and Evolution
, vol.27
, pp. 1877-1885
-
-
Lemey, P.1
Rambaut, A.2
Welch, J.J.3
Suchard, M.A.4
-
40
-
-
84895733259
-
Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2
-
Lemey, P., Rambaut, A., Bedford, T., Faria, N., Bielejec, F., Baele, G. et al. (2014) Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. PLoS Pathogens, 10, e1003932.
-
(2014)
PLoS Pathogens
, vol.10
, pp. e1003932
-
-
Lemey, P.1
Rambaut, A.2
Bedford, T.3
Faria, N.4
Bielejec, F.5
Baele, G.6
-
41
-
-
0037043652
-
Antiretroviral-drug resistance among patients recently infected with HIV
-
Little, S.J., Holte, S., Routy, J.P., Daar, E.S., Markowitz, M., Collier, A.C. et al. (2002) Antiretroviral-drug resistance among patients recently infected with HIV. New England Journal of Medicine, 347, 385-394.
-
(2002)
New England Journal of Medicine
, vol.347
, pp. 385-394
-
-
Little, S.J.1
Holte, S.2
Routy, J.P.3
Daar, E.S.4
Markowitz, M.5
Collier, A.C.6
-
42
-
-
80053436958
-
Host phylogeny determines viral persistence and replication in novel hosts
-
Longdon, B., Hadfield, J.D., Webster, C.L., Obbard, D.J. & Jiggins, F.M. (2011) Host phylogeny determines viral persistence and replication in novel hosts. PLoS Pathogens, 7, e1002260.
-
(2011)
PLoS Pathogens
, vol.7
, pp. e1002260
-
-
Longdon, B.1
Hadfield, J.D.2
Webster, C.L.3
Obbard, D.J.4
Jiggins, F.M.5
-
43
-
-
51249095575
-
Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species
-
Losos, J.B. (2008) Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters, 11, 995-1003.
-
(2008)
Ecology Letters
, vol.11
, pp. 995-1003
-
-
Losos, J.B.1
-
44
-
-
0026293261
-
Methods for the analysis of comparative data in evolutionary biology
-
Lynch, M. (1991) Methods for the analysis of comparative data in evolutionary biology. Evolution, 45, 1065-1080.
-
(1991)
Evolution
, vol.45
, pp. 1065-1080
-
-
Lynch, M.1
-
45
-
-
0030070991
-
Prognosis in HIV-1 infection predicted by the quantity of virus in plasma
-
Mellors, J.W., Rinaldo, Jr, C.R., Gupta, P., White, R.M., Todd, J.A. & Kingsley, L.A. (1996) Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science, 272, 1167-1170.
-
(1996)
Science
, vol.272
, pp. 1167-1170
-
-
Mellors, J.W.1
Rinaldo Jr, C.R.2
Gupta, P.3
White, R.M.4
Todd, J.A.5
Kingsley, L.A.6
-
46
-
-
34249986747
-
Prognostic value of HIV-1 RNA, CD4 cell count, and CD4 cell count slope for progression to aids and death in untreated HIV-1 infection
-
Mellors, J.W., Margolick, J.B., Phair, J.P., Rinaldo, C.R., Detels, R., Jacobson, L.P. & Muñoz, A. (2007) Prognostic value of HIV-1 RNA, CD4 cell count, and CD4 cell count slope for progression to aids and death in untreated HIV-1 infection. Journal of the American Medical Association, 297, 2349-2350.
-
(2007)
Journal of the American Medical Association
, vol.297
, pp. 2349-2350
-
-
Mellors, J.W.1
Margolick, J.B.2
Phair, J.P.3
Rinaldo, C.R.4
Detels, R.5
Jacobson, L.P.6
Muñoz, A.7
-
47
-
-
45849122039
-
Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics
-
Minin, V., Bloomquist, E. & Suchard, M. (2008) Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Molecular Biology and Evolution, 25, 1459-1471.
-
(2008)
Molecular Biology and Evolution
, vol.25
, pp. 1459-1471
-
-
Minin, V.1
Bloomquist, E.2
Suchard, M.3
-
48
-
-
76549254593
-
Notes on continuous stochastic phenomena
-
Moran, P. (1950) Notes on continuous stochastic phenomena. Biometrika, 37, 17-23.
-
(1950)
Biometrika
, vol.37
, pp. 17-23
-
-
Moran, P.1
-
49
-
-
84867402393
-
How to measure and test phylogenetic signal
-
Münkemüller, T., Lavergne, S., Bzeznik, B., Dray, S., Jombart, T., Schiffers, K. & Thuiller, W. (2012) How to measure and test phylogenetic signal. Methods in Ecology and Evolution, 3, 743-756.
-
(2012)
Methods in Ecology and Evolution
, vol.3
, pp. 743-756
-
-
Münkemüller, T.1
Lavergne, S.2
Bzeznik, B.3
Dray, S.4
Jombart, T.5
Schiffers, K.6
Thuiller, W.7
-
50
-
-
33747056328
-
Testing for different rates of continuous trait evolution using likelihood
-
O'Meara, B.C., Ané, C., Sanderson, M.J. & Wainwright, P.C. (2006) Testing for different rates of continuous trait evolution using likelihood. Evolution, 60, 922-933.
-
(2006)
Evolution
, vol.60
, pp. 922-933
-
-
O'Meara, B.C.1
Ané, C.2
Sanderson, M.J.3
Wainwright, P.C.4
-
51
-
-
84864697738
-
-
R package version 0.5.2.
-
Orme, D., Freckleton, R., Thomas, G., Petzoldt, T., Fritz, S., Isaac, N. & Pearse, W. (2013) caper: Comparative Analyses of Phylogenetics and Evolution in R. R package version 0.5.2. http://CRAN.R-project.org/package=caper.
-
(2013)
caper: Comparative Analyses of Phylogenetics and Evolution in R
-
-
Orme, D.1
Freckleton, R.2
Thomas, G.3
Petzoldt, T.4
Fritz, S.5
Isaac, N.6
Pearse, W.7
-
52
-
-
84921461472
-
-
Caper comparative analyses of phylogenetics and evolution in R.
-
Orne, D., Freckleton, R., Thomas, G., Petzoldt, T., Fritz, S., Issac, N. & Pearse, W. (2013) Caper comparative analyses of phylogenetics and evolution in R. http://CRAN.R-project.org/package=caper.
-
(2013)
-
-
Orne, D.1
Freckleton, R.2
Thomas, G.3
Petzoldt, T.4
Fritz, S.5
Issac, N.6
Pearse, W.7
-
53
-
-
0033613376
-
Inferring the historical patterns of biological evolution
-
Pagel, M. (1999) Inferring the historical patterns of biological evolution. Nature, 401, 877-884.
-
(1999)
Nature
, vol.401
, pp. 877-884
-
-
Pagel, M.1
-
54
-
-
1042304216
-
APE: analyses of phylogenetics and evolution in R language
-
Paradis, E., Claude, J. & Strimmer, K. (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
55
-
-
83855161149
-
-
R package version 3.1-113
-
Pinheiro, J., Bates, D., DebRoy, S., Sarkar, D. & R Core Team (2013) nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-113.
-
(2013)
nlme: Linear and Nonlinear Mixed Effects Models
-
-
Pinheiro, J.1
Bates, D.2
DebRoy, S.3
Sarkar, D.4
-
56
-
-
84866280221
-
Unifying the spatial epidemiology and molecular evolution of emerging epidemics
-
Pybus, O.G., Suchard, M.A., Lemey, P., Bernardin, F.J., Rambaut, A., Crawford, F.W., Gray, R.R., Arinaminpathy, N., Stramer, S.L., Busch, M.P. & Delwart, E.L. (2012) Unifying the spatial epidemiology and molecular evolution of emerging epidemics. Proceedings of the National Academy of Sciences of the United States of America, 109, 15066-15071.
-
(2012)
Proceedings of the National Academy of Sciences of the United States of America
, vol.109
, pp. 15066-15071
-
-
Pybus, O.G.1
Suchard, M.A.2
Lemey, P.3
Bernardin, F.J.4
Rambaut, A.5
Crawford, F.W.6
Gray, R.R.7
Arinaminpathy, N.8
Stramer, S.L.9
Busch, M.P.10
Delwart, E.L.11
-
57
-
-
84867364321
-
phytools: an R package for phylogenetic comparative biology (and other things)
-
Revell, L.J. (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217-223.
-
(2012)
Methods in Ecology and Evolution
, vol.3
, pp. 217-223
-
-
Revell, L.J.1
-
58
-
-
62949120782
-
Phylogenetic analysis of the evolutionary correlation using likelihood
-
Revell, L.J. & Collar, D.C. (2009) Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution, 63, 1090-1100.
-
(2009)
Evolution
, vol.63
, pp. 1090-1100
-
-
Revell, L.J.1
Collar, D.C.2
-
59
-
-
84865709842
-
A new bayesian method for fitting evolutionary models to comparative data with intraspecific variation
-
Revell, L.J. & Graham Reynolds, R. (2012) A new bayesian method for fitting evolutionary models to comparative data with intraspecific variation. Evolution, 66, 2697-2707.
-
(2012)
Evolution
, vol.66
, pp. 2697-2707
-
-
Revell, L.J.1
Graham Reynolds, R.2
-
60
-
-
84855283706
-
A new phylogenetic method for identifying exceptional phenotypic diversification
-
Revell, L.J., Mahler, D.L., Peres-Neto, P.R. & Redelings, B.D. (2012) A new phylogenetic method for identifying exceptional phenotypic diversification. Evolution, 66, 135-146.
-
(2012)
Evolution
, vol.66
, pp. 135-146
-
-
Revell, L.J.1
Mahler, D.L.2
Peres-Neto, P.R.3
Redelings, B.D.4
-
61
-
-
42349094829
-
The global circulation of seasonal influenza a (H3N2) viruses
-
Russell, C.A., Jones, T.C., Barr, I.G., Cox, N.J., Garten, R.J., Gregory, V. et al. (2008) The global circulation of seasonal influenza a (H3N2) viruses. Science, 320, 340-346.
-
(2008)
Science
, vol.320
, pp. 340-346
-
-
Russell, C.A.1
Jones, T.C.2
Barr, I.G.3
Cox, N.J.4
Garten, R.J.5
Gregory, V.6
-
62
-
-
78751478795
-
A Bayesian phylogenetic method to estimate unknown sequence ages
-
Shapiro, B., Ho, S.Y.W., Drummond, A.J., Suchard, M.A., Pybus, O.G. & Rambaut, A. (2011) A Bayesian phylogenetic method to estimate unknown sequence ages. Molecular Biology and Evolution, 28, 879-887.
-
(2011)
Molecular Biology and Evolution
, vol.28
, pp. 879-887
-
-
Shapiro, B.1
Ho, S.Y.W.2
Drummond, A.J.3
Suchard, M.A.4
Pybus, O.G.5
Rambaut, A.6
-
63
-
-
84896992703
-
How effectively can HIV phylogenies be used to measure heritability?
-
Shirreff, G., Alizon, S., Cori, A., Günthard, H.F., Laeyendecker, O., van Sighem, A., Bezemer, D. & Fraser, C. (2013) How effectively can HIV phylogenies be used to measure heritability? Evolution, Medicine and Public Health, 2013, 209-224
-
(2013)
Evolution, Medicine and Public Health
, vol.2013
, pp. 209-224
-
-
Shirreff, G.1
Alizon, S.2
Cori, A.3
Günthard, H.F.4
Laeyendecker, O.5
van Sighem, A.6
Bezemer, D.7
Fraser, C.8
-
64
-
-
3142682239
-
Mapping the antigenic and genetic evolution of influenza virus
-
Smith, D.J., Lapedes, A.S., de Jong, J.C., Bestebroer, T.M., Rimmelzwaan, G.F., Osterhaus, A.D.M.E. & Fouchier, R.A.M. (2004) Mapping the antigenic and genetic evolution of influenza virus. Science, 305, 371-376.
-
(2004)
Science
, vol.305
, pp. 371-376
-
-
Smith, D.J.1
Lapedes, A.S.2
de Jong, J.C.3
Bestebroer, T.M.4
Rimmelzwaan, G.F.5
Osterhaus, A.D.M.E.6
Fouchier, R.A.M.7
-
65
-
-
0034983646
-
Bayesian selection of continuous-time Markov chain evolutionary models
-
Suchard, M., Weiss, R. & Sinsheimer, J. (2001) Bayesian selection of continuous-time Markov chain evolutionary models. Molecular Biology and Evolution, 18, 1001-1013.
-
(2001)
Molecular Biology and Evolution
, vol.18
, pp. 1001-1013
-
-
Suchard, M.1
Weiss, R.2
Sinsheimer, J.3
-
66
-
-
21444440302
-
Models for estimating Bayes factors with applications in phylogeny and tests of monophyly
-
Suchard, M., Weiss, R. & Sinsheimer, J. (2005) Models for estimating Bayes factors with applications in phylogeny and tests of monophyly. Biometrics, 61, 665-673.
-
(2005)
Biometrics
, vol.61
, pp. 665-673
-
-
Suchard, M.1
Weiss, R.2
Sinsheimer, J.3
-
67
-
-
78149370844
-
Cohort profile: the Swiss HIV Cohort Study
-
Swiss HIV Cohort Study, Schoeni-Affolter, F., Ledergerber, B., Rickenbach, M., Rudin, C., Günthard, H.F., Telenti, A., Furrer, H., Yerly, S. & Francioli, P. (2010) Cohort profile: the Swiss HIV Cohort Study. International Journal of Epidemiology, 39, 1179-1189.
-
(2010)
International Journal of Epidemiology
, vol.39
, pp. 1179-1189
-
-
Schoeni-Affolter, F.1
Ledergerber, B.2
Rickenbach, M.3
Rudin, C.4
Günthard, H.F.5
Telenti, A.6
Furrer, H.7
Yerly, S.8
Francioli, P.9
-
68
-
-
0742325052
-
HLA allele sharing and HIV type 1 viremia in seroconverting zambians with known transmitting partners
-
Tang, J., Tang, S., Lobashevsky, E., Zulu, I., Aldrovandi, G., Allen, S., Kaslow, R.A. & Zambia-UAB HIV Research Project (2004) HLA allele sharing and HIV type 1 viremia in seroconverting zambians with known transmitting partners. AIDS Research and Human Retroviruses, 20, 19-25.
-
(2004)
AIDS Research and Human Retroviruses
, vol.20
, pp. 19-25
-
-
Tang, J.1
Tang, S.2
Lobashevsky, E.3
Zulu, I.4
Aldrovandi, G.5
Allen, S.6
Kaslow, R.A.7
-
69
-
-
84862764044
-
Bayesian models for comparative analysis integrating phylogenetic uncertainty
-
de Villemereuil, P., Wells, J.A., Edwards, R.D. & Blomberg, S.P. (2012) Bayesian models for comparative analysis integrating phylogenetic uncertainty. BMC Evolutionary Biology, 12, 102.
-
(2012)
BMC Evolutionary Biology
, vol.12
, pp. 102
-
-
de Villemereuil, P.1
Wells, J.A.2
Edwards, R.D.3
Blomberg, S.P.4
-
70
-
-
70349887757
-
Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target
-
Walker, L.M., Phogat, S.K., Chan-Hui, P.Y., Wagner, D., Phung, P., Goss, J.L. et al. (2009) Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target. Science, 326, 285-289.
-
(2009)
Science
, vol.326
, pp. 285-289
-
-
Walker, L.M.1
Phogat, S.K.2
Chan-Hui, P.Y.3
Wagner, D.4
Phung, P.5
Goss, J.L.6
-
71
-
-
77954943648
-
Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01
-
Zhou, T., Georgiev, I., Wu, X., Yang, Z.Y., Dai, K., Finzi, A. et al. (2010) Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science, 329, 811-817.
-
(2010)
Science
, vol.329
, pp. 811-817
-
-
Zhou, T.1
Georgiev, I.2
Wu, X.3
Yang, Z.Y.4
Dai, K.5
Finzi, A.6
|